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SeppeKuehnLab @seppekuehnlab.bsky.social · 12d

Schmidt AI + Science. Amazing fellowship opportunity at UChicago! apply.interfolio.com/173322

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

SeppeKuehnLab @seppekuehnlab.bsky.social · 22d

Great new paper from Kyle Crocker -- a talented postdoc in the group who is ** on the job market now ** !! @kylecrocker.bsky.social bsky.app/profile/kyle...

Kyle Crocker @kylecrocker.bsky.social · 22d

New paper out (doi.org/10.1093/isme...) with fantastic grad students Abby Skwara and Rathi Kannan! Advised by the excellent @seppekuehnlab.bsky.social and @amurugan.bsky.social. Overview in the thread below.

Timescale of environmental change modulates metabolic guild cohesion in microbial communities

Abstract. Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to lon

doi.org

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SeppeKuehnLab @seppekuehnlab.bsky.social · Sep 4

Center for Living Systems -- seeking strong post docs at the interface of physics and biology. Consider applying by Oct. 13! docs.google.com/forms/d/e/1F...

docs.google.com

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 31

Super well written and informative.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 12

Just cursor or copilot

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 12

For me, it speeds up coding by 10x easily. But it requires that you already know what you're doing with your data -- why, and how... and then requires validation. Clearly not a PhD in the pocket.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 12

Wait, this is news? Gulp.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 10

RevTex is far and away the best IMO.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 10

This important contribution sharpens the ill-defined concept of functional redundancy in microbial communities. It's a term we use a lot, but the exact meaning is elusive, and this paper is the first to sharpen it via proper null models. @ po-yi ho and KC Huang. www.sciencedirect.com/science/arti...

Challenges in interpreting functional redundancy and quantifying functional selection in microbial communities

Microbiomes often show similar functional profiles despite highly variable taxonomic compositions, a phenomenon attributed to “functional redundancy” …

www.sciencedirect.com

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Reposted by SeppeKuehnLab

NSF-Simons NITMB @nitmb.bsky.social · Aug 6

Mathematical Frameworks for Stability, Evolution, and Control in Microbial Communities

Explore new NITMB-Supported Research from @ssm57.bsky.social (Professor, University of Illinois Urbana-Champaign) and @seppekuehnlab.bsky.social (Associate Professor, University of Chicago)!

tinyurl.com/378ua7ws

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Reposted by SeppeKuehnLab

Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Aug 2

The “infer phenotypic traits” claim seems a bit of an overshoot given the training data does not include phenotypes. What we get is genomic patterns….and that itself can be super interesting, but the connect to phenotypes? How?

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Reposted by SeppeKuehnLab

Oded Rechavi @odedrechavi.bsky.social · Jul 31

🥂This was the highlight of my year. The "instigators", led by local master of the ceremony @svobodalab.bsky.social will never forget the privilege of organizing it and i think every participant will treasure the experience forever ❤️ @nature.com @josiegz.bsky.social www.nature.com/articles/d41...

Scientific bedlam at the world’s weirdest and wildest research conference

Woodstock Bio2 + Night Science aimed to encourage collaborations through creativity. The walk-on music for presentations was fun, too.

www.nature.com

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 28

Great thread! The sickle cell- malaria example blew me away and was news to me!

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 27

Few are as convincing as this one pubmed.ncbi.nlm.nih.gov/32669712/

A universal trade-off between growth and lag in fluctuating environments - PubMed

The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial resources, affecting, for example, the expression levels of proteins dedicated to metabolism and biosynt...

pubmed.ncbi.nlm.nih.gov

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Reposted by SeppeKuehnLab

Martina Dal Bello @martinadalbello.bsky.social · Jul 23

📢 We're seeking a postdoc to work on a project funded by HFSP @hfspo.bsky.social at the intersection of bacterial physiology, ecology and evolution. You can find more details about the project, the position, and how to apply here www.dalbellolab.com/hfsp-project! #bacteria #ecosky #MevoSky #microSky

HFSP project — dal bello lab

www.dalbellolab.com

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Reposted by SeppeKuehnLab

Dmitri Petrov @petrovadmitri.bsky.social · Dec 30

Excited to report that Joy Bergelson (bergelsonlab.org) and I will be running a brand new GRC conference on the Function of Evolving Systems in the summer of 2026. The 2028 one will be chaired by Mikhail Tikhonov (physics.wustl.edu/people/mikha...) and @asanchezlab.bsky.social! Stay tuned!

Faculty

physics.wustl.edu

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Reposted by SeppeKuehnLab

Daniel Cooney @danielcooney1.bsky.social · Jul 18

I am really happy to share that there will be a @nitmb.bsky.social workshop next year on mathematical and biological features of evolutionary game theory.

It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.

www.nitmb.org/evolutionary...

Evolutionary Games: Mathematical Theory and Biological Insights

www.nitmb.org

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 18

Story from UChicago press office - biologicalsciences.uchicago.edu/news/soil-mi...

Simple rules govern soil microbiome responses to environmental change

Research from UChicago shows how environmental changes lead to predictable responses in soil microbiome metabolism.

biologicalsciences.uchicago.edu

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Reposted by SeppeKuehnLab

Katherine Xue @ksxue.bsky.social · Jul 17

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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Reposted by SeppeKuehnLab

Nature @nature.com · Jul 17

Nature research paper: Functional regimes define soil microbiome response to environmental change

go.nature.com/3IqdJzd

Functional regimes define soil microbiome response to environmental change - Nature

Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynamics.

go.nature.com

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...

SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

THANKS! To all those involved and the work this was built on. Especially important for us were the classic Jim Tiedje papers of 80s and 90s and the work that started in our group with @karnagowda.bsky.social + Kyle Crocker.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

31 Finally - take the data seriously! The model hewed closely to the data – and as a result it made specific quantitive predictions. Right or wrong predictions are a necessity… Without them we will be stuck debating semantics. You often learn a lot (more!) from failed predictions too.

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SeppeKuehnLab @seppekuehnlab.bsky.social · Jul 17

30 Another lesson is to focus on function - sequencing and ‘omics technologies are high powered, but they can act like an out of control fire hose without a quantitative, often higher level, collective property of the system. This means not neglecting the ‘simple’ measurements.

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